Harvard anthropology professor Kimberly Theidon has a dossier of letters from the university attesting to her “outstanding achievement,” including when she was awarded one of a small number of endowed chairs for untenured professors and when she received an unusually large salary increase.

Theidon says she was told her department had voted unanimously to grant her tenure, and e-mails from colleagues described “stellar” reviews of her work from scholars in her field.

But none of that mattered in the end. Harvard turned down Theidon for tenure last spring, and she must depart the university at the end of the month.

To Theidon, the rejection was evidence of both gender discrimination and retaliation for her support of students victimized by sexual assault and sexual harassment, just as the university was facing a burgeoning student movement alleging the college was mishandling sexual assault cases. She filed a claim in March with the Massachusetts Commission Against Discrimination.

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Speaking on behalf of Harvard and president Drew Faust, who has the final say on tenure decisions, spokesman Jeff Neal said in a statement that Theidon’s allegations lack merit and that any advocacy work on her part “was not known, let alone considered, as part of the university’s decision on her tenure case.”

Theidon already has landed on her feet. After a fellowship next year, she will take up a faculty position at Tufts University’s Fletcher School.

Still, her case highlights one of the most difficult aspects of the struggle to combat a legacy of discrimination in the academic profession nationwide: Tenure is a secretive process. Candidates who are turned down for a lifetime appointment, the most central achievement in a professor’s career, generally never know why, whether the reason is legitimate concern about scholarship, discrimination of some stripe, or a petty grudge.

Denial of tenure is relatively common at elite universities like Harvard, and so are sore feelings and controversy within a department. Yet a complaint like Theidon’s is unusual, in part because most professors who are turned away prefer to quietly look for another job rather than risk the cost and embarrassment of a lawsuit or other public grievance.

Harvard is far from achieving equity for women faculty, nearly a decade after former president Lawrence H. Summers’s comments suggesting women have less aptitude for science brought passionate attention to the issue. Women make up only a quarter of Harvard’s tenured faculty, and 37 percent of junior faculty, according to the university’s data.

In the Faculty of Arts and Sciences, the central academic unit and where Theidon works, female professors had a 66 percent success rate gaining tenure in the last five years, compared to three-quarters of men.

And a faculty survey released last month found that female professors are less likely than their male counterparts to think that their school or department makes a genuine effort to recruit female professors or that the climate for women is as good as it is for men.

Statistics look similar at many institutions. Yet advocates for women and minorities rarely complain publicly about a specific tenure denial because it is so difficult to know why that decision was made.

“We never dealt with individual cases of tenure, because those are the really tough ones,” said Nancy Hopkins, an emeritus professor at Massachusetts Institute of Technology whose research on the disparities in how women with tenure were treated compared with men led MIT in 1999 to acknowledge pervasive discrimination.

Judicial interpretations in the last two decades have made it more difficult to win a tenure discrimination complaint, Mary Ann Mason wrote in the Chronicle of Higher Education in 2010. Mason, a professor at the University of California’s Berkeley School of Law who studies gender in academia, said a plaintiff has to prove not only that the reason given for tenure denial is untrue, but that the real reason is sex discrimination.

Yet some spurned candidates do find vindication. The MCAD last month upheld an earlier finding that Lulu C. H. Sun, an Asian woman who was tenured at the University of Massachusetts Dartmouth, was unfairly refused promotion to full professor. In 2010, after Emerson College denied tenure to two black professors, an external review found systemic biases at the college that undervalued African-Americans.

Theidon, who arrived at Harvard in 2004, is a medical anthropologist who studies Latin America and issues such as human rights and postwar reconciliation. One of her books inspired a 2009 film, “The Milk of Sorrow,” nominated for a foreign-language Academy Award, about the trauma women suffered under the reign of political violence in Peru.

Citing a slew of awards, publications, and glowing book reviews, Theidon’s lawyers, Elizabeth A. Rodgers and Philip J. Gordon, said they can prove that Theidon’s credentials are as strong as or stronger than other Harvard anthropologists who have been tenured, including a male professor who was recently granted tenure without having to submit to one of the usual stages of review.

Theidon said she felt for years that she was not treated as well as men in the department and recalls that the colleague who later chaired her tenure committee, Mary Steedly, had over the years made a number of comments telling her not to complain about perceived slights and to be a “dutiful daughter.”

In March 2013, as her tenure case was under consideration, Theidon posted comments supportive of sexual assault victims in the online discussion about an article in the student newspaper, the Harvard Crimson. A few weeks later, a former student came to Theidon upset about harassment by a faculty member, and Theidon suggested she speak with Steedly.

Soon, Steedly beckoned Theidon into her office and warned, “You are to be absolutely quiet about this. It’s a delicate time for you; your tenure hangs in the balance,” Theidon said.

The student, who spoke to the Globe on condition of anonymity, said Steedly also told her not to involve Theidon any further because it could affect her tenure review.

The student sent Theidon an e-mail in May 2013 saying, “they wanted to keep you out of it since your *bright destiny* here at Harvard still hangs in the balance.” The e-mail did not specify who the student was referring to.

Steedly wrote in an e-mail that she could not comment because of potential litigation.

After she was denied tenure in May 2013, Theidon said she complained to Judith D. Singer, Harvard’s senior vice provost for faculty development and diversity. Singer, she says, described some of the concerns of the secret group of administrators, plus scholars from Harvard and elsewhere, who reviewed her case after the anthropology department’s vote.

According to Theidon’s MCAD complaint, Singer said that group, called an ad hoc committee, discussed her “political activities” and indicated that those activities had been a substantial factor contributing to the denial of tenure. Theidon took that to mean her advocacy for students dealing with assault and harassment.

Singer also said that Theidon’s scholarly work in Spanish did not count toward tenure, Theidon says, and raised as a concern the fact that Theidon had not published in a particular anthropology journal.

Singer did not respond to requests for comment.

When Theidon was promoted in 2008, a letter from her department that was generally positive about her work made suggestions for additional steps she should take to earn tenure, including publishing articles in certain anthropology journals “recognized as the top outlets for social anthropology research.”

Theidon acknowledges not publishing in those journals, but said she was more interested in interdisciplinary outlets that would reach a broader audience. She called the suggestion that she needed certain journals an arbitrary standard not applied to others in her department.

Neal said “confidentiality is critical to Harvard’s tenure process” because the university relies on scholars sharing their unvarnished views. Still, he said in a statement, the standards for tenure are clear — and set an “exceptionally high” bar whereby “faculty members who are fine scholars and excellent teachers, but who are not judged likely to be ‘of the first order of eminence,’ do not become tenured professors.”

Gary Urton, chairman of the anthropology department, would not discuss the specifics of Theidon’s case, but said the department’s review of her was entirely “by the book.” While he was not privy to the subsequent review by the ad hoc committee, he said of the idea that Theidon suffered discrimination or retaliation, “I don’t believe it would happen.”

Theidon shared with the Globe e-mails from colleagues expressing dismay about the decision.

One colleague wrote that “only idiots or buffoons” would have ignored the “stellar” reviews written by experts in her field — letters that generally play an important role in a tenure decision.

Theidon noted that Harvard is being investigated by the federal Education Department’s Office for Civil Rights after students complained about violations of Title IX, a law governing how colleges handle sexual assault. She said she expects to have a great career without Harvard and sees a larger purpose in her complaint.

“It’s about the fact that that institution would prefer to deny tenure to an eminently qualified person rather than tenure that person and have her continue to speak out about how much they have failed to protect students, both women and men, on that campus,” Theidon said.

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